chr5-96662653-G-GGCAGGTGGCAGCAGGTGGCT
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001750.7(CAST):c.75+165_75+166insAGCAGGTGGCTGCAGGTGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 8284 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
CAST
NM_001750.7 intron
NM_001750.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.132
Genes affected
CAST (HGNC:1515): (calpastatin) The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1-4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 5-96662653-G-GGCAGGTGGCAGCAGGTGGCT is Benign according to our data. Variant chr5-96662653-G-GGCAGGTGGCAGCAGGTGGCT is described in ClinVar as [Benign]. Clinvar id is 1274367.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAST | NM_001750.7 | c.75+165_75+166insAGCAGGTGGCTGCAGGTGGC | intron_variant | ENST00000675179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAST | ENST00000675179.1 | c.75+165_75+166insAGCAGGTGGCTGCAGGTGGC | intron_variant | NM_001750.7 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 45722AN: 151612Hom.: 8268 Cov.: 0 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.302 AC: 45772AN: 151724Hom.: 8284 Cov.: 0 AF XY: 0.300 AC XY: 22253AN XY: 74136
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at